[2024-01-24 12:47:05,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,471] [INFO] DQC Reference Directory: /var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference
[2024-01-24 12:47:06,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,708] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg916d9308-0c70-4a4c-b0f8-4064086eb560/GCF_031458175.1_ASM3145817v1_genomic.fna.gz | prodigal -d GCF_031458175.1_ASM3145817v1_genomic.fna/cds.fna -a GCF_031458175.1_ASM3145817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:13,575] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:13,576] [INFO] Task started: HMMsearch
[2024-01-24 12:47:13,576] [INFO] Running command: hmmsearch --tblout GCF_031458175.1_ASM3145817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference/reference_markers.hmm GCF_031458175.1_ASM3145817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:13,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:13,775] [INFO] Found 6/6 markers.
[2024-01-24 12:47:13,796] [INFO] Query marker FASTA was written to GCF_031458175.1_ASM3145817v1_genomic.fna/markers.fasta
[2024-01-24 12:47:13,796] [INFO] Task started: Blastn
[2024-01-24 12:47:13,796] [INFO] Running command: blastn -query GCF_031458175.1_ASM3145817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference/reference_markers.fasta -out GCF_031458175.1_ASM3145817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:14,577] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:14,580] [INFO] Selected 25 target genomes.
[2024-01-24 12:47:14,581] [INFO] Target genome list was writen to GCF_031458175.1_ASM3145817v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:14,591] [INFO] Task started: fastANI
[2024-01-24 12:47:14,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg916d9308-0c70-4a4c-b0f8-4064086eb560/GCF_031458175.1_ASM3145817v1_genomic.fna.gz --refList GCF_031458175.1_ASM3145817v1_genomic.fna/target_genomes.txt --output GCF_031458175.1_ASM3145817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:27,085] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:27,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:27,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:27,102] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:27,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:27,102] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudoglutamicibacter cumminsii	strain=DSM 10493	GCA_016907775.1	156979	156979	type	True	85.032	580	740	95	below_threshold
Brevibacterium ravenspurgense	strain=CCUG56047	GCA_001584615.1	479117	479117	type	True	78.6775	63	740	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	78.0492	74	740	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	77.9952	77	740	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	77.6417	59	740	95	below_threshold
Glutamicibacter arilaitensis	strain=Re117	GCA_000197735.1	256701	256701	type	True	77.5759	92	740	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	77.5448	58	740	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.4853	79	740	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	77.4573	99	740	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	77.1967	87	740	95	below_threshold
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	77.0964	70	740	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	77.0117	79	740	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.0065	63	740	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	77.0014	88	740	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	76.9969	134	740	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	76.9299	73	740	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	76.8673	58	740	95	below_threshold
Galactobacter caseinivorans	strain=JZ R-183	GCA_003640665.1	2676123	2676123	type	True	76.787	104	740	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	76.7848	59	740	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	76.7819	56	740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:27,104] [INFO] DFAST Taxonomy check result was written to GCF_031458175.1_ASM3145817v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:27,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:27,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:27,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference/checkm_data
[2024-01-24 12:47:27,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:27,131] [INFO] Task started: CheckM
[2024-01-24 12:47:27,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458175.1_ASM3145817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458175.1_ASM3145817v1_genomic.fna/checkm_input GCF_031458175.1_ASM3145817v1_genomic.fna/checkm_result
[2024-01-24 12:47:51,941] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:51,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:51,961] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:51,961] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:51,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458175.1_ASM3145817v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:51,962] [INFO] Task started: Blastn
[2024-01-24 12:47:51,962] [INFO] Running command: blastn -query GCF_031458175.1_ASM3145817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5857d9a-1e79-4539-acf3-f404121cf38d/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458175.1_ASM3145817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:52,988] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:52,998] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:52,998] [INFO] Target genome list was writen to GCF_031458175.1_ASM3145817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:53,008] [INFO] Task started: fastANI
[2024-01-24 12:47:53,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg916d9308-0c70-4a4c-b0f8-4064086eb560/GCF_031458175.1_ASM3145817v1_genomic.fna.gz --refList GCF_031458175.1_ASM3145817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458175.1_ASM3145817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:00,181] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:00,193] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:00,193] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000758985.1	s__Pseudoglutamicibacter albus_A	98.1236	676	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudoglutamicibacter	95.0	98.46	98.42	0.96	0.96	3	conclusive
GCF_003143995.1	s__Pseudoglutamicibacter cumminsii_A	85.2991	571	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudoglutamicibacter	95.0	96.00	96.00	0.92	0.92	2	-
GCF_016907775.1	s__Pseudoglutamicibacter cumminsii	85.0631	580	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudoglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584615.1	s__Brevibacterium ravenspurgense	78.8769	64	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.93	96.42	0.92	0.90	8	-
GCF_001302565.1	s__Glutamicibacter halophytocola	77.9057	76	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.28	98.01	0.91	0.89	4	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	77.8409	94	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_014874065.1	s__Nesterenkonia halotolerans	77.5189	59	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017368795.1	s__PO-11 sp017368795	77.4477	62	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019173455.1	s__Nesterenkonia sp019173455	77.2059	58	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348945.1	s__Paeniglutamicibacter gangotriensis	77.0964	70	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	97.63	97.63	0.86	0.86	2	-
GCF_003575975.1	s__Galactobacter valiniphilus	76.9594	136	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003640665.1	s__Galactobacter caseinivorans	76.8099	103	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224415.1	s__Citricoccus sp000224415	76.5639	80	740	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	96.24	96.24	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:00,195] [INFO] GTDB search result was written to GCF_031458175.1_ASM3145817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:00,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:00,200] [INFO] DFAST_QC result json was written to GCF_031458175.1_ASM3145817v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:00,200] [INFO] DFAST_QC completed!
[2024-01-24 12:48:00,201] [INFO] Total running time: 0h0m55s